Real Me
by AnaCFranco
Summary: On a mission Skye is kidnapped by Hydra and everybody thinks she's dead. Now Skye will be forced to comply and fight against everyone she loves. Can the team break her out of the brainwash? Or did they lost Skye forever? Skyeward.
1. The Mission

**A/n:** New story. Let me know what do you guys think.

I hope you like it. Any feedback is appreciated and if anyone as any ideas on how I can make this story better plot wise and in my way of writing I would love to know.

I know the fight scenes are very good and detailed, I'm sorry I just really don't know how to write them.

Thanks to Gleek-Whovianfangirl for beta reading this.

 **Disclaimer:** I don't own Marvel's Agents of Shield.

* * *

Skye was sitting on the lounge room in the playground, trying to focus on the mission report she had to do but failing miserably due to the man on the other side of the room currently pretty much jumping in his seat over a game of battleship. She had to admit, it was hard to keep her distance like she was trying to, when he was being all nerdy and adorable.

Ward had been released form Vault D after two short months of imprisonment. While there, he had been reluctant to give any information to anyone but Skye even under May's 'interrogation technics' (which Skye hadn't known about until it was already too late to do anything to stop it), but after realizing the only way to start gaining everyone's forgiveness was to tell them everything he knew to whoever was willing to listen and the information started to come. Eventually Skye started to go down there as well, when Coulson made up some lame excuse as to why he couldn't do it himself, but Skye knew he was trying to give Ward some kind of reward for good behaviour. She limited to the questions about the mission, brushing off his worries about her with sharp words and hard looks. She made it clear that it wouldn't be as easy with her as it was with Coulson (who, with time started to go soft towards the former agent even as far as going after the truth about his past himself.)

This went on until one day Coulson announced he decided to release Grant from Vault D explaining that he was of more use to them in the field than locked up in a cell. Of course everybody thought he was losing it but since he was the director everybody sucked it up and learn to deal with Ward's presence. With time he did prove to be of more use out in the field. He proved that he was willing to die to protect everybody on the team, even the new guys that he didn't know that well.

With every mission he was in and every time he sacrificed himself, everybody started to trust him again and forgive him giving him another chance. Everybody but Skye. She thought that he had gotten off easy and she didn't want to trust him again. If necessary, she would do missions with him and be polite but she never let herself get close again with the fear that he might hurt her again like he did before.

But that started to get hard to do. Every time he risked his life for a member of the team. Every time he sacrificed himself for the mission, proving that he was willing to do anything to earn forgiveness, to earn back their trust.

Realizing that she couldn't spend the rest of her life holding a grudge and hating him, she decided to patch things up with him like everyone had already done. So they talked and decided to leave the past behind them and start over. After that they felt into an easy routine. They sparred, watched movies together, played battleship and soon enough Skye realized that this new Ward -the real Ward- is nothing like the stoic undercover persona he had pretended to be. This change didn't go unnoticed by Coulson who saw the potential in the pair and started to pair them up in the field.

For a while everything went well without a problem. But this is them they're talking about, so things had to eventually go wrong like it always did.

It happened when Skye's father came along, talking about evolution and destiny, and everything changed again. He kidnapped Skye and took her to some Hydra base and that's when everything really went wrong. In a turn of events Skye ended up in the tunnel under the base, some secret city and she went after after Raina to try to stop her and make things right but eneded up in the middle of an earthquake that almost ended her life. But still the same, there's no change, or evolution like her father had said would be.

Only when they are back at the base does she realize the change. How the ground shakes when she gets nervous or mad.

At first she keeps it to herself, afraid of what might happen if she reveals her new found abilities to the team, but Ward was quick to catch up with it and confront her about it. Surprisingly to Skye, he wasn't afraid, he's understanding and empathetic with her and promises not to tell anyone when she asks him not to.

After that she starts to push him away with fear that she might hurt him and despite the distance that she keeps between them, he keeps true to his words. But nobody in the team is dumb so they obviously put the pieces together and conclude that Skye was related to the earthquakes, that she's the one causing them.

Skye expects them to lock her away, to be scared of her, but they don't. Instead they try to help her figure out what triggered the earthquakes so that she can find a way to control them. FitzSimmons found out that her powers are strongly connected to her emotions.

With time she manages to get a hold of her powers and even managed to use them on some missions. But there were some things that could still set her off. That's why since then she decided to keep her distance from Ward.

Her feelings for him had been slowly intensifying since they had talked things through and she was afraid that if anything happened between her and Ward she would lose the little control she had over her powers.

But despite keeping her distance from him her feelings never changed, that's why Skye was finding it hard to focus on her work. Because every time she looked over at him she just wanted to cross the distance between them and kiss him senseless. But she knew she couldn't risk losing control and hurting people so she looked back at her computer and tried to focus on her work.

However she was once again stopped from doing so by Coulson walking into the room.

"Mission briefing in ten." He said before walking out of the room in a hurry.

Skye putted her laptop aside accepting that she wouldn't be able to get any work done that for the rest of the day and got up walking out of the lounge and into the conference room where almost everybody already was gathered. They waited until everybody was there and then Coulson started briefing.

"An agent was kidnapped from her safe house a week ago. We went there to see if we could recruit her back but she wasn't there. There were signs of what appears to be a fight. We know she was loyal to Shield and she would never willingly work for Hydra. But they have other ways of getting people to work for them."

"You mean brainwashing?" Ward asked.

Coulson nodded at that "We don't know if they were successful or not in brainwashing her though."

"So we don't know what we're walking into." May finished.

Coulson nodded once again.

"But if Whitehall is dead then the brainwashing is ineffective, right?" Simmons asked.

"We don't know." Coulson answered. "All we know is that someone took over and Hydra is still running. We managed to get the location of where they kept our agent but we don't have much more than that."

"So we're going in blind." Bobbi said.

"It wouldn't hurt to try and find out a little more about it." He said looking pointedly at Bobbi.

"I'll see what I can do." She answered, understanding what he was referring to, before walking out the door going to Vault D where Bakshi was imprisoned.

The rest of the team stayed in the conference room waiting to hear the rest of Coulson's orders

"We're going to break into the compound so we'll need the entire team on this mission. Skye and Ward will be in charge of getting to the agent and assess the situation… It's important that we get her out of there alive. Not only does she have intel on Hydra, but it's also our job to help a fellow agent out."

Skye and Ward nodded at that and Coulson took that as his cue to continue.

"May and I will try to get to whoever is in charge and take them down and Bobbi, Mack, Trip and Hunter are in charge of clearing the place up, FitzSimmons will stay on the van running comms."

They all just nodded in understanding and then cleared out of the room, going they separate ways to prepare for the mission.

Skye was in the armory gearing up when Ward walked in and starting to gear up himself.

"Do you think we'll get to her in time?" Skye asked after a few minutes breaking the silence between them.

"I don't know." He answered truthfully "But even if we don't, we'll do all that we can to help her."

"I can't imagine what that must be like. Forgetting everything about yourself. Following someone blindly without even knowing why you're doing, just that you have to."

"I know." He said "Don't worry, we'll get to her and then we'll help her."

"Let's hope so."

"Hey." He said putting a hand on her arm in a comforting manner. "You don't have to worry about anything going wrong, I've got your back, OK?"

Skye softened a little at that and nodded saying "And I've got yours." Before walking out of the room leaving Ward to finish gearing up by himself.

Breaking into the compound wasn't hard to do and soon Skye and Ward where navigating through the halls taking out any agents that came in their way until they came across the agent in question.

"Agents 33, we're here to help you." Ward said, pointing his ICER at her in case he needed to take her out.

"I don't need your help." She said before lunging at them.

Ward and Skye simply tried to block her mover knowing they couldn't take her out. After a while Ward managed to knock her out but before they could get out of the building with the agent, more Hydra agents got in their way making it impossible for them to get out of there.

"I got this. Just get her out of here." Skye said moving to face the agents.

"Skye..." Ward started to protest but she stopped him from doing so.

"Ward, I got this! Just go!"

Ward reluctantly got out of the building with the unconscious agent in his arms and, thankfully didn't find any more agents, and moved to the van where Fitz, Simmons and Mack were.

""Is she..." Jemma started when he laid the agent down.

"She's unconscious." He finished for her understanding her question. "Hydra managed to brainwash her so I had no knock her out. Now I need to go help Skye." He said and he was once again out of the van moving inside the building only to see Coulson, May, Bobbi, Hunter and Trip running out of it.

"What's going on?" Ward asked alarmed, stopping in front of them.

"It was a trap. The building is set to blow up, we need to get out of here. Did you and Skye get agent 33?" Coulson asked.

"What!? Skye is still in the building, we need to get her." Ward said running to get back inside.

But before he could get there the compound blew up making the ground beneath them shake.

"Skye!" Ward screamed trying to run to the building once again but he was stopped from doing so by Coulson grabbing his arm.

"Ward, you can't go in there." Coulson told him calmly.

"What!? Are you insane!? Skye is in there. We need to get her. We need to help her." Ward said looking in at Coulson like he had gone insane.

"Ward, the building is being consumed by the flames. There's no way she..."

"No!" he interrupted him, tears starting to wheel up in his eyes "It can't be..."

"I know." Coulson said also on the verge of tears while Ward looked helplessly at the building.

"We have to go." May spoke up in a sad tone.

Coulson nodded and they all reluctantly moved back to the van still not believing Skye was gone.

"We heard an explosion, what happened?" Simmons asked when they were all inside the van only then realizing that Skye wasn't with them and asked "Where is Skye?"

Coulson looked at her sadly and explained "It was a trap. The compound was set up to blow up, Skye was still in there when it happened. I'm sorry Simmons."

"What!? No, it can't be, that can't be true." Simmons said and she started crying.

"I'm so sorry Simmons." Coulson said again, embracing the younger agent and letting his own tears fall for the girl he had always viewed as a daughter.

* * *

Skye had finally managed to knock the last agent down and was finally moving out of the compound to meet with Ward and FitzSimmons in the van when she was stopped by more agents on her way.

"Damn it!" She cursed before lunging into action, fighting the Hydra agents with everything that she got to take them down.

She had managed to take two of them down but when she was about to go for the third guy she felt something hit her on the back of the head making her go down and lose consciousness.

The last thing she was aware of was someone lifting her up and carrying her, she supposed, out of the building and then she fell under.


	2. Happy To Comply

**A/N:** Thank you to everyone who followed, favorited and left comments, it means a lot to know people are liking this story.

Feedback is always appreciated. If anyone has any suggestion on how I get this story plot wise and in my way of writing I'm happy to hear it.

Also, I'm sorry it took so long to update but I had some trouble with the brainwash scene and I still don't really like how it turned out.

Disclaimer: I don't own Marvel's Agents of S.H.I.E.L.D..

* * *

The ride back to the base was made in silence after Jemma's sobs had eventually quieted down. Everyone was still in shock and no one could believe what had happened. No one could believe that Skye was gone just like that. Skye of all people. She always had such a strong presence and now she was just gone, leaving a hole in the team. How could they move forward? How would they be able to cope with it? Things would never be the same again without Skye around. But they had to keep trying to take down hydra if anything to get justice for Skye.

When they arrived to the base a moment later, they got agent 33 out of the van and put her in a vault so they could assess her situation before interrogating her and trying to start helping her when she woke up.

After that they all went to the playground's conference room to the debrief, all of them still shaken up by what happened on the mission.

"I know we're all still in shock by what happened on the mission, I still can't believe it myself, but we have to keep going. We need to keep going after Hydra and take them down. To get justice for Skye. Make sure her death wasn't for nothing." Coulson said when everyone was there.

Fitz shook his head.

"We don't even know if she's really dead. We didn't see the body. We have no proof that she is dead so she could still be alive." He said not wanting to believe his friend was really dead.

"Fitz" Coulson sighed "There's no way she could have survived that explosion. We have to accept what happened."

"We don't actually know that for sure, sir." Jemma spoke up backing up her friend "I mean, we never even found out the extents of her abilities or even if she had more than one. She could have survived thanks to them."

"It's still a long shot, Jemma." Coulson tried to reason with them in a sad tone not letting himself believe in something that may not actually happen.

"If I could just go back there, maybe I could analyze the bodies and find out if any of them belongs to Skye. And even if it is her, we could bring the body and have a funeral." Jemma suggested hoping that her friend was somehow still alive even though she knew the chances of that happening where slim.

"I don't think it's safe to go back there." Coulson replied.

"Why not? Hydra must have cleaned out before the explosion. The only people there left are the ones that were expendable to them and I'm pretty sure they're long dead." Ward spoke up trying to reason with him.

"Ok." Coulson relented turning to Simmons "You and Fitz can go back and analyze the place. May and Hunter will go with you just in case you encounter someone unexpected."

"Yes, sir. We'll just go get our equipment and then we'll go." Jemma said before leaving the room to go to the lab with Fitz following right behind her.

"And the rest of us, sir? What do we do in the mean time?" Ward asked.

"Agent 33 must be waking up soon. I would like you to go and try to interrogate her." He said before turning to Bobbi. "Agent Morse, I would like you to try and interrogate Bakshi again. See if he may know who the new leader of Hydra is and where their new base of operations may be."

They both nodded in confirmation before they both went their separate ways.

Bobbi went down to Vault D to interrogate Bakshi hoping that this time she would manage to get the intel they needed to stop Hydra and hoping that this time he would be more cooperative.

When she got down there he was lying in the cot placed in the corner of the room but got up when he heard her come down the stairs.

"Back already?" He asked sarcastically.

"You didn't really gave me the information we needed last time so..." Bobbi trailed off sitting down on the chair across from him.

"And I'm not gonna give you anything. So your trip down here was waste of time." he said sitting up.

"I don't get it. How can you be so loyal to Hydra? I mean, they couldn't even bothered to come for you." She replied in disbelief, not understanding how he could be so loyal to someone who just abandoned him like that.

"Is that supposed to convince me to tell you everything you need?" He asked her in a mocking tone.

"I'm just saying, maybe you're not as important to Hydra as we thought or even as you thought you were."

"Then maybe you shouldn't be interrogating me, since I don't matter."

"Nice try. But you still have intel that we need. So you should start talking. You can start by telling me who might be the new head of Hydra."

"New head?" Bakshi asked, confused.

"Yeah. Did I forget to tell you? Whitehall is dead." She said faking confusion.

"That's funny." He said with a dry laugh.

"I'm not joking. Coulson put a bullet in his head. I saw the body myself."

"That's not what I meant. What I meant was that it's funny that you think he's dead. That a simple bullet would be able to stop him."

"What do you mean by that? Whitehall is alive?" She asked, confused.

"Indeed. Doctor Whitehall is not an easy man to kill. He has certain... abilities and can heal better than others do."

"How can he do that?"

"Perhaps you should ask Agent Skye."

"Skye?" She asked, "How could she know about that? What does Skye have to do with Whitehall?"

"Not her. Her mother."

"Her mother?" She asked again, still confused before it dawned on her "Her mother had powers like her. What did Whitehall do to her? Did he kill her?"

"He did, but before that he did something much worse. He opened her up, tore her apart."

"And why did he do that? Besides his perverted way of thinking."

"Discovery requires experimentation." He replied simply.

"Cut the Hydra crap and answer my question."

"He did it so he, let's say, could restore himself. He cut her open and transplanted some of her organs into himself. Consequently he obtained the same powers as her."

"What powers exactly?"

"She didn't age and she healed more easily than normal people do."

"So he gained her abilities?"

"Indeed." He nodded.

"Well, thank you for telling me all we needed to know. Looks like you told me everything I wanted to know after all."

And then she got up heading up the stairs going to Coulson's office to tell him everything she had learned hoping it would be helpful to get Whitehall.

Meanwhile Ward was in another vault where they had locked agent 33 up and was waiting for her to wake up so he could assess the situation so they could decide how to proceed and what was the best way to help her.

He knew that locking her up wasn't the best way to convey their intentions but they didn't know how she would react when she woke up so they had no other choice.

The vault was similar to Vault D where he had been locked up and where Bakshi was now locked up.

Agent 33 was laying on the cot in the corner of the room while he sat in front of the cell wall.

He couldn't stop thinking about what had happened in the mission. He still couldn't believe that Skye was really gone. And couldn't stop thinking that maybe it was his fault. After all, if he hadn't left her behind and helped her fight those Hydra agents she might still be there with them. Fitz and Simmons still hope that she was alive but he just couldn't. He couldn't let himself hope like that. He rather face the reality now.

And that reality was that Skye was gone. They would never see her again. He would never hear her voice or talk with her again. He would never be able to tell her how he really felt. Because despite everything that happened he had never stopped loving her, he just never had the courage to tell her, and now he never would.

He was pulled out of his thoughts by a groan coming from in front of him. Looking up he saw that Agent 33 was awake and was sitting up on the bed.

She looked around taking in the room before her eyes settled on him.

"Where am I?" She asked in a panicked tone.

"Agent 33." Ward started getting up from the chair and walking closer to the laser grid, "I'm Agent Grant Ward. You're in S.H.I.E.L.D.'s custody."

"S.H.I.E.L.D.? No it can't be. He's gonna kill me." She murmured the last part to herself.

"Who? The man you get your orders from? Who is he?"

"You might as well kill me already because I'm not gonna give you anything." She said instead of answering his questions.

"We're not gonna kill you, we just want to help you."

"I don't need your help."

"I know it's hard to believe, but you were once a S.H.I.E.L.D. agent and I like to believed you can still be one, if you let us help you."

"What? No, I was never loyal to S.H.I.E.L.D., I'm loyal to hydra and to Doctor Whitehall."

"Wait, Whitehall? That's impossible, he's dead."

"He's not dead. I receive my orders directly from him."

"So he's the one who..." he trailed off before muttering to himself "I have to tell Coulson."

And then he was bolting up the stairs going straight to Coulson's office and entered, not even bothering to knock.

"Sir, I know who's leading Hydra."

"Whitehall." Coulson said nodding in confirmation.

Only then did Ward looked around noticing Bobbi was also in the room.

"Bakshi pretty much told me everything we needed to know." She clarified.

"So what do we do? How do we get him?" Ward asked.

"First we wait for FitzSimmons to return. If Skye is in fact alive then we'll still have some time to rescue her before it's too late, if Whitehall plans to do what agent Morse think he does."

"What's your theory?" he asked her turning his attention to her.

And then Bobbi started to explain what she thought Whitehall wanted to do with Skye, from the conversation she had with Bakshi.

The first thing Skye noticed when she regained consciousness was that both her wrists and legs were cuffed up to something and even head was being held in place. She tried to move her wrist to see if she could get free but it was to no use since the restraints were too tight. She kept her eyes closed all the while and tried to not move too much so if there was someone in the room she wouldn't alert them on being awake. She tried to listen for any sound to find out if anyone was there and when she heard no sound she opened her eyes looking around the room, taking it all in and seeing if there was any way she could escape finding it to be impossible.

A moment later she heard the door to the room open but before she could fake still being unconscious someone spoke up letting her know they knew she was conscious.

"I see you're finally awake." She heard, recognizing the male voice but being able to remember who it belonged to.

But before she could put a name to the voice the man stepped into her line of vision making her gasp in shock.

She couldn't believe what she was seeing. She thought he was dead and he was supposed to be dead. She saw his dead body. It wasn't possible.

"That's impossible. You were dead." She said in disbelief.

"Maybe Agent Coulson should check twice before assuming someone is dead." He replied, sarcastically.

"He put a bullet through your head. You should be dead."

"Let's just say that your mother's ability help a lot with that." He said, smugly.

"Is that why you kidnapped me? You're gonna do to me what you did you her?" She asked, knowing well what he had done to her mother thanks to her father's disturbing description of it.

"At first that was what I planned to do, but then I saw your abilities and I realized that you would be of more use to me alive, working in the field."

"I would rather die before working for you or Hydra." Skye spat out angrily.

"Oh, believe me. In time you will." He said with a knowing smile, "And you will become a valuable member of our organization."

He then turned away from her and said "Let's get started, I have a feeling we'll be here for a while."

Then, a monitor was turned up in front of her drawing her attention.

Whitehall came closer to her and said in an almost soothing tone "Surrender and you will find meaning. Take a deep breath and calm your mind. Your compliance will be rewarded."

She could feel herself slipping away but she tried to resist the best she could. She thought about the team knowing that they would do everything they could to get her back and that soon it would all be over.

"Are you ready to comply, Agent Skye?" He asked a moment later.

"Screw you." she spat out.

"I knew it wouldn't be easy. But don't worry, we have plenty of time." He told her and stepped away a little.

She doesn't know how much time passes after that. But as it passes, with him spilling Hydra's mottos and beliefs, she can feel herself slipping away no matter how much she tries to resist. And she knows that it's not worth it so she gives up giving into that state of hypnosis until she can't take it anymore and loses consciousness.

She doesn't remember anything before this moment, as she wakes up on a bed of what she assumes is a hospital room. She sits up and looks around taking in the room she's in. She concludes then that she's not really in a hospital but it's clear that she's in some sort of medical bay, of what she doesn't know.

She also can't remember anything prior to waking up and worse, who she is which is a little troubling, to say the least. Had she lost her memories in an accident of some sort? Why wasn't she in a hospital then? Who had brought her there? All those questions and she had no one to answer them.

A moment later though, a man walked in to the room with a triumphant look on his face.

"Who are you? Where am I? Why am I here?" She asked in one breath before he could say anything.

"I'm doctor Whitehall." He introduced himself calmly before asking, "What do you remember, exactly?"

She frowned at the question before answering "Nothing. I don't even remember who I am. What happened? Did I get in some kind of accident?"

"You can say that." He replied.

"What do you want from me?" She asked, starting to get alarmed.

"Just calm down." He said taking a step forward, "Take a deep breath and clear your mind."

She did as she was told knowing it would do her no good to get worked up.

"Good. That's it." He said in soothing tone, "Your compliance will be rewarded."

She felt like something clicked in her brain at those words. It was like all the questions she had before didn't matter anymore.

"Are you ready to comply?" He asked a moment later, seeing a change in her expression.

"Yes, sir." She replied without a second thought.

"Good. There's a change of clothes for you. Get dressed and then meet me in my office. I want you to get started as soon as possible."

"Happy to comply."


End file.
